# Computers in Scientific Discovery 6

21-25 August 2012
Portorož, Slovenia
UTC timezone
Home > Contribution List
Displaying 48 contributions out of 48
Type: Oral presentation
Several optimization techniques have been developed in the past for optimizing various real-life problems we encounter during logistic operations. The quality and applicability of the results depend on the quality of input data as the famous saying "garbage in - garbage out" applies here more than anywhere. With input data we consider here quality of digital maps, accessibility and quality of GPS ... More
Presented by Dr. Alen ORBANIć
Type: Oral presentation
Association schemes are background combinatorial objects in the area of Algebraic Graph Theory (AGT). The main well-known origin of models for association schemes, the so-called Schurian association schemes, appears from transitive permutation groups by taking their 2-orbits (orbitals). All association schemes of order up to 14 can be obtained in this manner. It turns out that not all asso ... More
Presented by Dr. Štefan GYüRKI
Type: Oral presentation
House of Graphs (http://hog.grinvin.org) is a searchable database of graphs. It offers lists of graphs and generators but also a special list of graphs that turned out to be interesting or relevant in the study of graph theoretic problems or as counterexamples to conjectures. A prototype of this project was first presented in the previous edition of CSD (Computers in Scientific Discovery 5, Sheffi ... More
Type: Oral presentation
An $n\times n\times n$ cube is made from $n^3$ unit cubes. Two such cubes are neighbours if they touch along a face. In each step of a dismantling process, we may remove a small cube that has precisely three neighbours. A move is {\it balanced} if the three neighbours are in three orthogonal directions. In the extremal case, there are $n^2$ independent small cubes left at the end of the d ... More
Presented by Dr. Janos BARAT
Type: Oral presentation
Carbon cages which violate the isolated pentagon rule or have an open-shell electronic system can be stabilized to be isolable by an appropriate endohedral or exohedral functionalization. Such an example is the observation of the C28 cluster with Td symmetry with an encapsulated uranium atom. A systematic study of classical fullerenes, i.e. containing only pentagons and hexagons, with tetrahedral ... More
Presented by Dr. Levente Csaba NAGY
Type: Oral presentation
This talk will discuss the construction and classification of configurations by computers. Results and conjectures will be presented. An early result was obtained for cubic graphs on 10 vertices (which were needed for applications in chemistry) in the 1960s by Balaban and Imrich. The same result had already be obtained at the end of the 19th century in the language of configurations, of course wi ... More
Presented by Harald GROPP
Type: Keynote Lecture
An arc is a set of points in a projective plane with the property that no three of them are on the same line. An arc is called complete if no point can be added to it so that it still remains an arc. The conic serves as the standard example of a complete arc, but many other constructions are known. Although arcs are relatively small (at most q+2 points in a finite projective plane of order q an ... More
Presented by Prof. Kris COOLSAET
Type: Oral presentation
Cloud computing is fundamentally changing how computing resources are being delivered. The end-users increasingly access cloud-based applications using remote web-services, standard web browsers or “native applications” that just pretend to be more than a web browser. Infrastructure, databases and software are being deployed in a way that can be used as a service (rented) when needed. At the s ... More
Presented by Dr. Boris HORVAT
Type: Oral presentation
In the simplest case, a geometric $(n_k)$ configuration is a set of $n$ points and $n$ lines such that each of the points is incident with precisely $k$ of the lines and each of the lines is incident with precisely $k$ of the points. Instead of lines, the second subset can consist of planes, hyperplanes, circles, ellipses, etc. We present some new classes of highly symmetric spatial point-line co ... More
Presented by Dr. Gábor GéVAY
Type: Keynote Lecture
One of the promising fields in linguistics deals with the 'meanings' of sentences and words. In the present talk two cases will be discussed to show how various computer methods can be applied to the linguistic problems. The first case shows is the use of Kohonen Self-organizing maps- SOM (a special method of Artificial neural networks (ANNs) for studying and comparison of different styles of writ ... More
Presented by Prof. Jure ZUPAN
Type: Keynote Lecture
The standard model of molecule (on the topological level of abstraction) is an unlabeled colored multigraph, expressing by its nodes the atoms, by its (multiple) edges the covalent bonds. The nodes are colored by atom names and states. But there are problems, the model expresses pairwise interactions only, so the notion of aromaticity shows that it should be generalized, maybe to a hypergraphic mo ... More
Type: Oral presentation
Coherent configurations (Higman, Weisfeiler-Leman) are a central notion in Algebraic Graph Theory. An important class of coherent configurations - the so-called Schurian configurations - are obtained from the 2-orbits of permutation groups of finite degree. However in general, coherent configurations are non-Schurian. Important invariants of coherent configurations are their types; they ... More
Presented by Dr. Sven REICHARD
Type: Oral presentation
We show that if an $n$-edge cut divides a graph into two subgraphs, then the Tutte polynomial of the original graph can be fully expressed by Tutte polynomials of these parts. We give a formula consisting from a determinant of size $1+b_{n}$ (where $b_{n}$ is the $n$th Bell number). The edge cut induces a bipartite graph with partition of vertices of size $p$ and $p'$. Our second formula uses dete ... More
Presented by M. KOCHOL
Type: Oral presentation
There are nowadays many automated systems [3] helping researchers in graph theory, such as Graffiti (1987) [2], AutoGraphiX (AGX) (2000) [1] and Graphedron (2008) [4]. However, no system has been developed for directed graphs. Moreover, as most of existing systems use exact (and costly in time) algorithms, new approaches are needed. We introduce here <i>Digenes</i>, a new tool for directed extr ... More
Presented by Mr. Romain ABSIL
Type: Keynote Lecture
The traditional allotropic forms of carbon, multilayer graphene and diamond, are “honorary hydrocarbons” with huge numbers of carbon atoms surrounded by a negligible number of hydrogen atoms. Enumerations of benzenoids should consider both definitions, including or excluding helicenes. Dualists offer simple classifications for catafusenes, perifusenes, and coronoids as having acyclic, triangul ... More
Presented by Prof. Balaban ALEXANDRU
Type: Poster
Purine, as a mother template of important nucleobases, is the good model system to study such properties of these systems as pi-electron delocalization and interactions with acidic or basic partners. For this purpose, modeling of equilibrium H-bond formation of the types N…HF and NH…F– was used [1]. H-bonded complexes of purine (four complexes for each tautomer: 1-H, 3-H, 7-H and 9-H puri ... More
Presented by Dr. Halina SZATYLOWICZ
Type: Oral presentation
We describe a new algorithm for the efficient generation of fullerenes. The algorithm generates all non-isomorphic fullerenes using the construction operations from [1]. We will describe the construction, provide details on the way isomorphism rejection is handled, and give some optimizations. Our implementation of this algorithm is more than 3 times faster than previous generators for fullerenes. ... More
Presented by Mr. Jan GOEDGEBEUR
Type: Oral presentation
Encyclopedia of Graphs (http://atlas.gregas.eu/) is an online encyclopedia of graph collections aiming to help researchers find and use data about different families of graphs. It has been created as a part of the ESF funded GreGAS project with the goal of becoming a general reference and repository of graphs and graph-like structures offered to all scientists and researchers for use and to provid ... More
Presented by Dr. Primož LUKšIč
Type: Oral presentation
A Delaney-Dress symbol is a structure that encodes an equivariant tiling, i.e. tilings together with their symmetry groups. In this talk we will describe a generator for Delaney-Dress symbols and thus for tilings. We will give an introduction to Delaney-Dress symbols and discuss the structural properties that are used by the generation algorithm. We will also present some results already obtained ... More
Presented by Mr. Nico VAN CLEEMPUT
Type: Oral presentation
We investigate the structure of trees that have minimal $k$-th Laplacian and Dirichlet Eigenvalues among all trees with a given degree sequence.
Presented by Dr. Matjaž KOVšE
Type: Keynote Lecture
The concept of communicability between pairs of nodes in a graph is introduced. Then, the communicability distance is defined and it is proved that it corresponds to a Euclidean distance in the graph. The mathematical expressions for the communicability distance between pairs of nodes in paths, cycles, stars and complete graphs are obtained as well as the expressions for the sum of all distances i ... More
Type: Oral presentation
1. Introduction An interesting aspect of finite-length carbon nanotubes (CNTs) is the quantum finite-size effects of the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). It has been shown that the HOMO-LUMO gaps in the zigzag CNTs show the oscillation depending on the number of hexagons around the peripheral circuits. We have sh ... More
Presented by Dr. Noriyuki MIZOGUCHI
Type: Oral presentation
A {\it fullerene} is an all carbon molecule that can be represented by a $3$-regular planar graph with face sizes five or six. A subset $S$ of the vertices of a graph forms an {\it independent set} if the vertices of $S$ are pairwise non-adjacent. This talk describes chemical applications for independent sets of fullerenes and algorithms for generating them.
Presented by Dr. Wendy MYRVOLD
Type: Poster
For a graph $G=(V,E)$, \emph{a Roman dominating function} (RDF) is a function $f \colon V \to \{0,1,2\}$ satisfying the condition that every vertex $u$ for which $f(u)=0$ is adjacent to at least one vertex $v$ for which $f(v)=2$. The weight of an RDF equals $w(f)=\sum_{v\in V}f(v)=|V_1|+2|V_2|$. An RDF for which $w(f)$ achieves its minimum is called \emph{a} $\gamma_R$\emph{-function} and its weig ... More
Presented by Ivona PULJIć
Type: Keynote Lecture
How many large eigenvalues can a graph have? An answer depends on the interpretation of what it means for en eigenvalue to be large. This question and some related problems in extremal algebraic graph theory will be discussed.
Presented by Bojan MOHAR
Type: Poster
Aromaticity is an important and widely used concept characterizing properties and structure of many organic and inorganic chemical compounds [1–3]. Environmental effects can lead to significant structural alterations of molecules directly exposed to environment. Such changes are of particular interest in molecules important from a biochemical perspective. All nucleobases and four amino acid res ... More
Presented by Dr. Beata SZEFLER
Type: Keynote Lecture
Aromaticity is an elusive chemical concept, with many definitions, but it does have at least one clear manifestation in ‘ring currents’ induced in planar unsaturated molecules by perpendicular magnetic fields. Efficient ab initio calculation of such currents is now a practical possibility. The resulting current-density maps allow us to visualise aromaticity and to develop interpretations and t ... More
Presented by Prof. Patrick FOWLER
Type: Oral presentation
Molecular dynamics calculations can reveal the physical and chemical properties of various carbon nanostructures or can help to devise the possible formation pathways. In our days the most well known carbon nanostructures are the fullerenes and the nanotubes. They can be thought of as being formed from graphene sheets, i.e. single layers of carbon atoms arranged in a honeycomb lattice. Usuall ... More
Presented by Dr. Istvan LASZLO
Type: Poster
Mathchem is a free open source Python package for calculating topological indices and other invariants of molecular graphs. For performance reasons we use here concept of lazy calculations. This means that we calculate data only when it is needed and then we save the results. Mathchem can be installed either as Python or as Sage module. Since the package contains no compiled code it is cross-pl ... More
Presented by Mr. Alexander VASILYEV
Type: Oral presentation
The minimum genus problem is a classical, but NP-complete problem in topological graph theory. Minimum genus of cartesian products is closely related to the minimum genus of a group, the minimum among genera of all Cayley graphs of the given group. For abelian groups, the most difficult case arises when the group contains a Z_3 factor in its canonical decomposition. In this talk we focus main ... More
Presented by Michal KOTRBčIK
Type: Oral presentation
In chemical graph theory a topological index is a molecular descriptor that is calculated on the basis of molecular graph of a chemical compound. They are used for example in QSAR approach in which the biological activity of molecules is correlated with their chemical structure. The bibliographic data on topological indices were obtained from Web of Science, an online citation database for scient ... More
Presented by Jernej BODLAJ
Type: Oral presentation
The Zentralblatt MATH Database stores metadata about mathematical papers and books. It is maintained by the Berlin editorial ooffice of FIZ Karlsruhe in cooperation with European academies and mathematical institutes. We analyzed the ZB data about scientific works published within the period 1990 to 2010. The raw data were converted into four 2-mode networks: works x authors, works x journals, ... More
Presented by Ms. Monika CERINšEK
Type: Oral presentation
In approximation theory, it is well known that the bivariate polynomial interpolation problem at domain points of a triangle is correct. Thus the corresponding interpolation matrix M is nonsingular. L.L. Schumaker stated the conjecture, that the determinant of M and all principal minors of M are positive. This result would solve the constrained interpolation problem. In this talk, the basic con ... More
Type: Keynote Lecture
Graphs can be drawn in an infinite number of ways. However, by analysis of eigenvectors of adjacency and Laplacian matrices of molecular graphs one is able to get drawings which reproduce rather well geometries in some classes of molecules like fullerenes, nanotubes and their junctions. The results obtained up to now will be discussed and possible new routes to generalize graph drawing techniques ... More
Presented by Prof. Ante GRAOVAC
Type: Oral presentation
We present a new parallelized algorithm, Parallel-ProBiS, for detecting similar binding sites on clusters of computers. This is a new algorithm that calcu- lates the local similarity metric between protein structures, and is especially suited to efficient execution on multiple CPUs. The obtained speedups of the parallel ProBiS scale almost ideally with the number of computing cores up to about 64 ... More
Presented by Ms. Kati ROZMAN
Type: Oral presentation
POLYBENZENES AND RELATED NANOSTRUCTURES Mircea V. Diudea “Babes-Bolyai” University, Faculty of Chemistry and Chemical Engineering, Arany Janos Str. 11, 400028, Cluj, Romania diudea@gmail.com Abstract. Polybenzene BTA_48 (Figure), designed by map operations, can dimerize either by identification of octagons R(8) to provide a diamond-like fcc-net or by identifying the “opening ... More
Presented by Prof. Mircea DIUDEA
Type: Oral presentation
A \emph{combinatorial configuration} $(v_r, b_k)$ is an incidence structure with $v$ points and $b$ blocks (called lines) such that each point is incident with $r$ lines, each line is incident with $k$ points and two distinct lines are incident with at most one common point. When $v = b$ (and consequently $r = k$) we speak of \emph{symmetric} or \emph{balanced} $(v_r)$ configurations. One of th ... More
Presented by Mr. Marko BOBEN
Type: Keynote Lecture
Chemical Graph Theory is concerned with analysis of chemical data using Discrete Mathematics and Graph Theory. Graphical Bioinformatics approaches problems of Bioinformatics by representing input data graphically and follows with their numerical analysis. We will consider recent developments in these areas including: (1) Novel graph matrices and novel graph invariants; (2) Graph theoretical calc ... More
Presented by Prof. Milan RANDIć
Type: Keynote Lecture
A Latin square of order $n$ is an $n\times n$ matrix containing $n$ different symbols (often the numbers $1,\dots,n$), positioned in such a way that each symbol occurs exactly once in each row and exactly once in each column. Latin squares have numerous applications in design of experiments, schedules for sporting tournaments, codes for communication and so on. In this talk I will consider, f ... More
Presented by Ian WANLESS
Type: Keynote Lecture
Fluency in a language is fundamental to an understanding of any culture and the struggle to develop the language of the Sciences, mathematics and related symbolism, proved to be unnaturally difficult. In fact Science was born around the time of the 16th Century as a consequence of a new philosophical approach which required evidence for the validation of all claims without exception. This way of ... More
Presented by Prof. Harold KROTO
Type: Keynote Lecture
In this talk I will sketch an algorithm to generate Snarks -- that is cubic cyclically 4-connected graphs with chromatic index 4. Snarks are especially interesting as for several conjectures it can be shown that if they wrong, the smallest counterexample is a Snark. I will also give some examples of conjectures that were refuted with the lists generated by the algorithm. As we are now able ... More
Presented by Gunnar BRINKMANN
Type: Keynote Lecture
Community detection is an important part of the analysis of naturally occuring networks. The quality of division into communities is measured mostly by modularity, representing the difference from the expected number of edges occuring within and between the communities. Here we reinterpret modularity within a more general framework for measuring the quality of community division and discuss on rea ... More
Presented by Prof. Dragan STEVANOVIć
Type: Keynote Lecture
\begin{abstract} \noindent Many Problems in Computational Geometry and geometric Graph Theory are based on the most simple geometric objects: points in the plane and straight line segments connecting them. Moreover, for most combinatorial questions in this area only the discrete'' properties of the underlying point set have to be considered. More precisely, the crossing prop ... More
Presented by Prof. Oswin AICHHOLZER
Type: Keynote Lecture
Molecular stability and electronic degeneracy do not form an evident combination. In degenerate states of highly symmetric molecules, there is a mismatch between the symmetries of electronic and nuclear charge distributions. This imbalance gives rise to a spontaneous distortion of the nuclear frame to a lower symmetry, which lifts the degeneracy. The effect is known as the Jahn-Teller (JT) effect. ... More
Presented by Prof. Arnout CEULEMANS
Type: Oral presentation
A matrix $A \in \mathbb{R}^{n \times n}$ is a Euclidean distance matrix (EDM) if there exist points $x_1, x_2, \dots, x_n \in \mathbb{R}^d$, such that $a_{ij} = ||x_i - x_j||^2$. The minimal possible $d$ is called the embedding dimension. A well known result states that the rank of an EDM is $d + 2$ for the points in a general position, and $d + 1$ if the points lie on a $d - 1$ dimensional hype ... More
Presented by Dr. Iztok KAVKLER
Type: Oral presentation
The Hückel–London–Pople–McWeeny (HLPM) (‘Topological’) approach1–4 for calculating π-electron ring-currents and bond-currents in conjugated systems is applied to a series of structures that have been called ‘super-ring’ molecules5. These consist of an outer ring of carbon atoms (of perimeter length either [4n] or [4n+2]) connected by internal C–C bonds to an inner, central ring ... More
Presented by Dr. Roger MALLION
Type: Poster
In this work we investigate the problem of numerical characterization of two dimensional proteomics maps based on construction of Voronoi regions. To enable for the taking into account of the concentrations of proteins on the proteomic map, we have used the process which gives greater weights to spots representing proteins with greater abundance. As we have shown, the shapes of the resulting Voro ... More
Presented by Rok OREL
Type: Oral presentation
In 1845, as a 21-year-old undergraduate, Gustav Robert Kirchhoff (writing under the pseudonym ‘Studiosus’ Kirchhoff) published, as ‘Mitglied des physikalischen Seminars zu Königsberg’ at the Albertina University, a classic paper1 in which he stated his Laws I and II of electrical circuits — laws which, for more than a century, have been ‘well-known to every schoolboy’. Two years la ... More
Presented by Dr. Roger MALLION